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47 lines
1.6 KiB
Text
47 lines
1.6 KiB
Text
process SAMTOOLS_MARKDUP {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0':
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'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
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input:
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tuple val(meta), path(input)
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path fasta
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output:
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tuple val(meta), path("*.bam"), emit: bam, optional: true
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tuple val(meta), path("*.cram"), emit: cram, optional: true
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tuple val(meta), path("*.sam"), emit: sam, optional: true
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def reference = fasta ? "--reference ${fasta}" : ""
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def extension = args.contains("--output-fmt sam") ? "sam" :
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args.contains("--output-fmt bam") ? "bam" :
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args.contains("--output-fmt cram") ? "cram" :
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"bam"
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if ("$input" == "${prefix}.${extension}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
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"""
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samtools \\
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markdup \\
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$args \\
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${reference} \\
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-@ $task.cpus \\
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-T $prefix \\
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$input \\
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${prefix}.${extension}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
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END_VERSIONS
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"""
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}
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